The high cost of processor fabrication plants and approaching physical limits have started a new wave research in alternative computing paradigms. As an alternative to the top-down manufactured silicon-based computers, research in computing using natural and physical system directly has recently gained a great deal of interest. A branch of this research promotes the idea that any physical system with sufficiently complex dynamics is able to perform computation. The power of networks in representing complex interactions between many parts make them a suitable choice for modeling physical systems. Many studies used networks with a homogeneous structure to describe the computational circuits. However physical systems are inherently heterogeneous. We aim to study the effect of heterogeneity in the dynamics of physical systems that pertains to information processing. Two particularly well-studied network models that represent information processing in a wide range of physical systems are Random Boolean Networks (RBN), that are used to model gene interactions, and Liquid State Machines (LSM), that are used to model brain-like networks. In this thesis, we study the effects of function heterogeneity, in-degree heterogeneity, and interconnect irregularity on the dynamics and the performance of RBN and LSM. First, we introduce the model parameters to characterize the heterogeneity of components in RBN and LSM networks. We then quantify the effects of heterogeneity on the network dynamics. For the three heterogeneity aspects that we studied, we found that the effect of heterogeneity on RBN and LSM are very different. We find that in LSM the in-degree heterogeneity decreases the chaoticity in the network, whereas it increases chaoticity in RBN. For interconnect irregularity, heterogeneity decreases the chaoticity in LSM while its effects on RBN the dynamics depends on the connectivity. For {K} < 2, heterogeneity in the interconnect will increase the chaoticity in the dynamics and for {K} > 2 it decreases the chaoticity. We find that function heterogeneity has virtually no effect on the LSM dynamics. In RBN however, function heterogeneity actually makes the dynamics predictable as a function of connectivity and heterogeneity in the network structure. We hypothesize that node heterogeneity in RBN may help signal processing because of the variety of signal decomposition by different nodes.

Mapping dynamical motion to neural brain activity is one of many challenges in the field of neuroscience. Further knowledge in this area could provide useful insights in fields such as medical treatment of brain disorders. However, progress in the field is halted by the immense complexity of the human brain and the diversity of unique dynamical behaviours. In this project the stereotypical grooming behaviour of mice is analysed to gain knowledge of its dynamical features. Properties such as the dimensionality of the underlying dynamical system and trajectories of state space reconstructions are analysed using tools such as Taken's delayed embedding theorem, Principal Component Analysis and Locally Linear Embedding. / Att sammankoppla motorik med hjärnans neurala aktivitet är en av många utmaningar inom neurovetenskapen. En bättre förståelse inom området kan vara till stor nytta för behandling av till exempel neurologiska sjukdomar. Komplexiteten av den mänskliga hjärnan och den stora mängden av unika rörelsebeteenden gör dock processen svårare. I det här projektet analyseras det stereotypiska skötselbeteendet hos möss för att få en djupare förståelse om dess dynamiska egenskaper. Dimensionaliteten av skötselbeteendet och rekonstruktioner av det dynamiska flödet undersöks med hjälp av exempelvis Taken's delayed embedding Theorem, Principal Component Analysis och Locally Linear Embedding.

No / We show that the multidimensional Zeno effect combined with non-holonomic control allows one to efficiently protect quantum systems from decoherence by a method similar to classical random coding. The method is applicable to arbitrary error-inducing Hamiltonians and general quantum systems. The quantum encoding approaches the Hamming upper bound for large dimension increases. Applicability of the method is demonstrated with a seven-qubit toy computer.

Starting from the observation that substances and reactions are the central entities of chemistry, I have structured chemical knowledge into a formal space called a directed hypergraph, which arises when substances are connected by their reactions. I call this hypernet chemical space. In this thesis, I explore different levels of description of this space: its evolution over time, its curvature, and categorical models of its compositionality. The vast majority of the chemical literature focuses on investigations of particular aspects of some substances or reactions, which have been systematically recorded in comprehensive databases such as Reaxys for the last 200 years. While complexity science has made important advances in physics, biology, economics, and many other fields, it has somewhat neglected chemistry. In this work, I propose to take a global view of chemistry and to combine complexity science tools, modern data analysis techniques, and geometric and compositional theories to explore chemical space. This provides a novel view of chemistry, its history, and its current status. We argue that a large directed hypergraph, that is, a model of directed relations between sets, underlies chemical space and that a systematic study of this structure is a major challenge for chemistry. Using the Reaxys database as a proxy for chemical space, we search for large-scale changes in a directed hypergraph model of chemical knowledge and present a data-driven approach to navigate through its history and evolution. These investigations focus on the mechanistic features by which this space has been expanding: the role of synthesis and extraction in the production of new substances, patterns in the selection of starting materials, and the frequency with which reactions reach new regions of chemical space. Large-scale patterns that emerged in the last two centuries of chemical history are detected, in particular, in the growth of chemical knowledge, the use of reagents, and the synthesis of products, which reveal both conservatism and sharp transitions in the exploration of the space. Furthermore, since chemical similarity of substances arises from affinity patterns in chemical reactions, we quantify the impact of changes in the diversity of the space on the formulation of the system of chemical elements. In addition, we develop formal tools to probe the local geometry of the resulting directed hypergraph and introduce the Forman-Ricci curvature for directed and undirected hypergraphs. This notion of curvature is characterized by applying it to social and chemical networks with higher order interactions, and then used for the investigation of the structure and dynamics of chemical space. The network model of chemistry is strongly motivated by the observation that the compositional nature of chemical reactions must be captured in order to build a model of chemical reasoning. A step forward towards categorical chemistry, that is, a formalization of all the flavors of compositionality in chemistry, is taken by the construction of a categorical model of directed hypergraphs. We lifted the structure from a lineale (a poset version of a symmetric monoidal closed category) to a category of Petri nets, whose wiring is a bipartite directed graph equivalent to a directed hypergraph. The resulting construction, based on the Dialectica categories introduced by Valeria De Paiva, is a symmetric monoidal closed category with finite products and coproducts, which provides a formal way of composing smaller networks into larger in such a way that the algebraic properties of the components are preserved in the resulting network. Several sets of labels, often used in empirical data modeling, can be given the structure of a lineale, including: stoichiometric coefficients in chemical reaction networks, reaction rates, inhibitor arcs, Boolean interactions, unknown or incomplete data, and probabilities. Therefore, a wide range of empirical data types for chemical substances and reactions can be included in our model.

Accelerating the simulation of turbulence to stationarity is a critical challenge in various engineering applications. This study presents an innovative equation-free multiscale approach combined with a machine learning technique to address this challenge in the context of the one-dimensional stochastic Burgers' equation, a widely used toy model for turbulence. We employ an encoder-decoder recurrent neural network to perform super-resolution reconstruction of the velocity field from lower-dimensional energy spectrum data, enabling seamless transitions between fine and coarse levels of description. The proposed multiscale-machine learning framework significantly accelerates the computation of the statistically stationary turbulent Burgers' velocity field, achieving up to 442 times faster wall clock time compared to direct numerical simulation, while maintaining three-digit accuracy in the velocity field. Our findings demonstrate the potential of integrating equation-free multiscale methods with machine learning methods to efficiently simulate stochastic partial differential equations and highlight the possibility of using this approach to simulate stochastic systems in other engineering domains. / Master of Science / In many practical engineering problems, simulating turbulence can be computationally expensive and time-consuming. This research explores an innovative method to accelerate these simulations using a combination of equation-free multiscale techniques and deep learning. Multiscale methods allow researchers to simulate the behavior of a system at a coarser scale, even when the specific equations describing its evolution are only available for a finer scale. This can be particularly helpful when there is a notable difference in the time scales between the coarser and finer scales of a system. The ``equation-free approach multiscale method coarse projective integration" can then be used to speed up the simulations of the system's evolution. Turbulence is an ideal candidate for this approach since it can be argued that it evolves to a statistically steady state on two different time scales. Over the course of evolution, the shape of the energy spectrum (the coarse scale) changes slowly, while the velocity field (the fine scale) fluctuates rapidly. However, applying this multiscale framework to turbulence simulations has been challenging due to the lack of a method for reconstructing the velocity field from the lower-dimensional energy spectrum data. This is necessary for moving between the two levels of description in the multiscale simulation framework. In this study, we tackled this challenge by employing a deep neural network model called an encoder-decoder sequence-to-sequence architecture. The model was used to capture and learn the conversions between the structure of the velocity field and the energy spectrum for the one-dimensional stochastic Burgers' equation, a simplified model of turbulence. By combining multiscale techniques with deep learning, we were able to achieve a much faster and more efficient simulation of the turbulent Burgers' velocity field. The findings of this study demonstrated that this novel approach could recover the final steady-state turbulent Burgers' velocity field up to 442 times faster than the traditional direct numerical simulations, while maintaining a high level of accuracy. This breakthrough has the potential to significantly improve the efficiency of turbulence simulations in a variety of engineering applications, making it easier to study and understand these complex phenomena.

Komplexe Netzwerke sind mächtige Werkzeuge, die die Untersuchung komplexer Systeme unterstützen. In vielen Bereichen werden komplexe Netzwerke eingesetzt, um die Dynamik interagierender Entitäten wie Neuronen, Menschen oder sogar Wettersysteme zu verstehen. Darüber hinaus erweitern sich die Anwendungsbereiche mit der stetigen Entwicklung neuer theoretischer Ansätze. In dieser Arbeit wollen wir sowohl den theoretischen Rahmen der Netzwerkwissenschaften weiterentwickeln als auch komplexe Netzwerke in der Klimatologie und der computergestützten Sozialwissenschaft anwenden. / Complex networks are powerful tools enabling the study of complex systems. In many fields, complex networks are used as a tool to gain an understanding of the dynamics of interacting entities such as neurons in a brain, humans on social media, or global weather systems. At the same time, new theoretical frameworks that extend the toolbox of Network Science promote the application of network tools in new research fields. In this thesis, we aim for both, advancing the theoretical framework of Network Science as well as applying complex networks in Climatology and Computational Social Science.

Die Modellierung komplexer Systeme mit einer großen Anzahl von Freiheitsgraden ist in den letzten Jahrzehnten zu einer großen Herausforderung geworden. In der Regel werden nur einige wenige Variablen komplexer Systeme in Form von gemessenen Zeitreihen beobachtet, während die meisten von ihnen - die möglicherweise mit den beobachteten Variablen interagieren - verborgen bleiben. In dieser Arbeit befassen wir uns mit dem Problem der Rekonstruktion und Vorhersage der zugrunde liegenden Dynamik komplexer Systeme mit Hilfe verschiedener datengestützter Ansätze. Im ersten Teil befassen wir uns mit dem umgekehrten Problem der Ableitung einer unbekannten Netzwerkstruktur komplexer Systeme, die Ausbreitungsphänomene widerspiegelt, aus beobachteten Ereignisreihen. Wir untersuchen die paarweise statistische Ähnlichkeit zwischen den Sequenzen von Ereigniszeitpunkten an allen Knotenpunkten durch Ereignissynchronisation (ES) und Ereignis-Koinzidenz-Analyse (ECA), wobei wir uns auf die Idee stützen, dass funktionale Konnektivität als Stellvertreter für strukturelle Konnektivität dienen kann. Im zweiten Teil konzentrieren wir uns auf die Rekonstruktion der zugrunde liegenden Dynamik komplexer Systeme anhand ihrer dominanten makroskopischen Variablen unter Verwendung verschiedener stochastischer Differentialgleichungen (SDEs). In dieser Arbeit untersuchen wir die Leistung von drei verschiedenen SDEs - der Langevin-Gleichung (LE), der verallgemeinerten Langevin-Gleichung (GLE) und dem Ansatz der empirischen Modellreduktion (EMR). Unsere Ergebnisse zeigen, dass die LE bessere Ergebnisse für Systeme mit schwachem Gedächtnis zeigt, während sie die zugrunde liegende Dynamik von Systemen mit Gedächtniseffekten und farbigem Rauschen nicht rekonstruieren kann. In diesen Situationen sind GLE und EMR besser geeignet, da die Wechselwirkungen zwischen beobachteten und unbeobachteten Variablen in Form von Speichereffekten berücksichtigt werden. Im letzten Teil dieser Arbeit entwickeln wir ein Modell, das auf dem Echo State Network (ESN) basiert und mit der PNF-Methode (Past Noise Forecasting) kombiniert wird, um komplexe Systeme in der realen Welt vorherzusagen. Unsere Ergebnisse zeigen, dass das vorgeschlagene Modell die entscheidenden Merkmale der zugrunde liegenden Dynamik der Klimavariabilität erfasst. / Modeling complex systems with large numbers of degrees of freedom have become a grand challenge over the past decades. Typically, only a few variables of complex systems are observed in terms of measured time series, while the majority of them – which potentially interact with the observed ones - remain hidden. Throughout this thesis, we tackle the problem of reconstructing and predicting the underlying dynamics of complex systems using different data-driven approaches. In the first part, we address the inverse problem of inferring an unknown network structure of complex systems, reflecting spreading phenomena, from observed event series. We study the pairwise statistical similarity between the sequences of event timings at all nodes through event synchronization (ES) and event coincidence analysis (ECA), relying on the idea that functional connectivity can serve as a proxy for structural connectivity. In the second part, we focus on reconstructing the underlying dynamics of complex systems from their dominant macroscopic variables using different Stochastic Differential Equations (SDEs). We investigate the performance of three different SDEs – the Langevin Equation (LE), Generalized Langevin Equation (GLE), and the Empirical Model Reduction (EMR) approach in this thesis. Our results reveal that LE demonstrates better results for systems with weak memory while it fails to reconstruct underlying dynamics of systems with memory effects and colored-noise forcing. In these situations, the GLE and EMR are more suitable candidates since the interactions between observed and unobserved variables are considered in terms of memory effects. In the last part of this thesis, we develop a model based on the Echo State Network (ESN), combined with the past noise forecasting (PNF) method, to predict real-world complex systems. Our results show that the proposed model captures the crucial features of the underlying dynamics of climate variability.

Det finns ett stort behov av elektrifiering av transportsektorn då en offensiv klimatpolitik ställer höga krav på minskade utsläpp från personbilar. För att lyckas med övergången till en fordonsflotta med lägre koldioxidutsläpp, är utbyggnad av den publika laddningsinfrastrukturen en nyckelfaktor. Den publika laddningsinfrastrukturenär ett komplext system där aktörer måste överväga relationer med flera aktörer, och kan därmed betraktas ur ett affärsekosystemsperspektiv. Studien syftar således till att öka förståelsen för publik laddningsinfrastruktur i Sverige utifrån ett affärsekosystemsperspektiv, och hur tillväxtpotentialen kan förbättras för att möjliggöra en framgångsrik övergång till elfordon. Studien är av explorativ karaktär och har samlat in data för att besvara studiens syfte genom en empirisk fallstudie, semistrukturerade intervjuer och en litteraturöversikt. Resultatet indikerar att de största utmaningarna för utvecklingen av publik laddningsinfrastruktur är att affärsekosystemet är fragmenterat, det finns avsaknad av standarder, och det råder brist på kapacitet i det svenska elnätet. Majoriteten av utmaningarna anses däremot vara möjliga att lösa genom samevolution. Som stöttepelare är det laddstationsoperatörens uppgift är att utforma strategier som gynnar samtliga samarbetspartners, och således samevolution. På grund av systemets framväxande karaktär bör laddstationsoperatörer även eftersträva färre, men starkare sammanlänkade, samarbetspartners. Vidare bör beslutsfattare se över regleringar och lagar som inte är anpassade för samhällets elektrifiering, och förslagsvis bevilja undantag för frågor som berör publik laddningsinfrastruktur. Genom bidrag och stöd kan beslutsfattare även möjliggöra självorganisering, och således utveckling av publik laddningsinfrastruktur. I takt med att marknaden mognar bör beslutsfattarnas involvering minska i syfte att öka affärsekosystemets självorganisering, effektivitet och produktivitet. Denna studie bidrar till teorin genom att utifrån ett affärsekosystemsperspektiv öka förståelsen för hur organisationer som är omslutande av ett sammanlänkat system integrerar i sina gemensamma ansträngningar för att uppnå en framgångsrik övergång till elfordon. / An offensive climate policy places a high demand on reducing emissions from passenger cars. Consequently, there is an urgency for an electrified transport sector. The expansion of the public charging infrastructure is a key success factor for the transition toward a vehicle fleet with lower carbon dioxide emissions. However, the public charging infrastructure is a complex system where organisations must consider relationships with companies from different industries and can advantageously be viewed from a business ecosystem perspective. Hence, the purpose of this study is to increase the understanding of the public charging infrastructure in Sweden from a business ecosystem perspective, and how the growth potential can be improved to enable an increased transition to electric vehicles. To fulfill the purpose, an exploratory study has been conducted, and data has been collected through an extensive empirical case study, semi-structured interviews, and a review of existing literature. The results indicate that the lack of capacity in the Swedish electricity network, the fragmented business ecosystem, and the lack of standards, are the biggest obstacles to the development of the public charging infrastructure. These challenges can partly be managed through coevolution. As a keystone player, the charge point operator has a responsibility to effectively create strategies that benefit all partners. Due to the emerging and agile nature of the system, charge point operators should further strive for fewer, and strongly linked partnerships. Furthermore, decision- and policymakers should review regulations and policies associated with the electrification of society, and grant exceptions concerning the public charging infrastructure. In addition, they can enable the development of public charging infrastructure, through grants and support. However, as the public charging infrastructure matures, decision makers' involvement should decrease to increase the business ecosystem's self-organisation, efficiency, and productivity. This study contributes to theory by increasing the understanding of how organisations integrate their joint efforts, to achieve a transition, from a businessecosystem perspective.

El uso de las redes para modelar sistemas complejos es creciente en multitud de ambitos. Son extremadamente utiles para representar interacciones entre genes, relaciones sociales, intercambio de informaci on en Internet o correlaciones entre precios de acciones burs atiles, por nombrar s olo algunos ejemplos. Analizando la estructura de estas redes, comprendiendo c omo interaccionan sus distintos elementos, podremos entender mejor c omo se comporta el sistema en su conjunto. A menudo, los nodos que conforman estas redes tienden a formar grupos altamente conectados. Esta propiedad es conocida como estructura de comunidades y esta tesis doctoral se ha centrado en el problema de c omo mejorar su detecci on y caracterizaci on. Como primer objetivo de este trabajo, se encuentra la generaci on de m etodos e cientes que permitan caracterizar las comunidades de una red y comprender su estructura. Segundo, pretendemos plantear una serie de pruebas donde testar dichos m etodos. Por ultimo, sugeriremos una medida estad stica que pretende ser capaz de evaluar correctamente la calidad de la estructura de comunidades de una red. Para llevar a cabo dichos objetivos, en primer lugar, se generan una serie de algoritmos capaces de transformar una red en un arbol jer arquico y, a partir de ah , determinar las comunidades que aparecen en ella. Por otro lado, se ha dise~nado un nuevo tipo de benchmarks para testar estos y otros algoritmos de detecci on de comunidades de forma e ciente. Por ultimo, y como parte m as importante de este trabajo, se demuestra que la estructura de comunidades de una red puede ser correctamente evaluada utilizando una medida basada en una distribuci on hipergeom etrica. Por tanto, la maximizaci on de este ndice, llamado Surprise, aparece como la estrategia id onea para obtener la partici on en comunidades optima de una red. Surprise ha mostrado un comportamiento excelente en todos los casos analizados, superando cualitativamente a cualquier otro m etodo anterior. De esta manera, aparece como la mejor medida propuesta para este n y los datos sugieren que podr a ser una estrategia optima para determinar la calidad de la estructura de comunidades en redes complejas. / Aldecoa García, R. (2013). Detección de comunidades en redes complejas [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/31638 / Premios Extraordinarios de tesis doctorales

Doctor of Philosophy / Computing and Information Sciences / Scott A. DeLoach / As sensor prices drop and computing devices continue to become more compact and powerful, computing capabilities are being embedded throughout our physical environment. Connecting these devices in cyber-physical systems (CPS) enables applications with significant societal impact and economic benefit. However, engineering CPS poses modeling, architecture, and engineering challenges and, to fully realize the desired benefits, many outstanding challenges must be addressed. For the cyber parts of CPS, two decades of work in the design of autonomous agents and multiagent systems (MAS) offers design principles for distributed intelligent systems and formalizations for agent-oriented software engineering (AOSE). MAS foundations offer a natural fit for enabling distributed interacting devices. In some cases, complex control structures such as holarchies can be advantageous. These can motivate complex organizational strategies when implementing such systems with a MAS, and some designs may require agents to act in multiple groups simultaneously. Such agents must be able to manage their multiple associations and assignments in a consistent and unambiguous way. This thesis shows how designing agents as systems of intelligent subagents offers a reusable and practical approach to designing complex systems. It presents a set of flexible, reusable components developed for OBAA++, an organization-based architecture for single-group MAS, and shows how these components were used to develop the Adaptive Architecture for Systems of Intelligent Systems (AASIS) to enable multigroup agents suitable for complex, multigroup MAS. This work illustrates the reusability and flexibility of the approach by using AASIS to simulate a CPS for an intelligent power distribution system (IPDS) operating two multigroup MAS concurrently: one providing continuous voltage control and a second conducting discrete power auctions near sources of distributed generation.